Partners in crime: Proteins implicated in RNA repeat expansion diseases

Abstract

Short tandem repeats are repetitive nucleotide sequences robustly distributed in the human genome. Their expansion underlies the pathogenesis of multiple neurological disorders, including Huntington's disease, amyotrophic lateral sclerosis, and frontotemporal dementia, fragile X-associated tremor/ataxia syndrome, and myotonic dystrophies, known as repeat expansion disorders (REDs). Several molecular pathomechanisms associated with toxic RNA containing expanded repeats (RNA^exp ) are shared among REDs and contribute to disease progression, however, detailed mechanistic insight into those processes is limited. To deepen our understanding of the interplay between toxic RNA^exp molecules and multiple protein partners, in this review, we discuss the roles of selected RNA-binding proteins (RBPs) that interact with RNA^exp and thus act as "partners in crime" in the progression of REDs. We gather current findings concerning RBPs involved at different stages of the RNA^exp life cycle, such as transcription, splicing, transport, and AUG-independent translation of expanded repeats. We argue that the activity of selected RBPs can be unique or common among REDs depending on the expanded repeat type. We also present proteins that are functionally depleted due to sequestration on RNA^exp within nuclear foci and those which participate in RNA^exp -dependent innate immunity activation. Moreover, we discuss the utility of selected RBPs as targets in the development of therapeutic strategies. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.

Keywords: RAN translation; RNA binding proteins; liquid-liquid phase separation; repeat expansion; short tandem repeats.

FIGURE 1

Characteristics of expanded STRs specific for different diseases. (a) Localization and size of STRs within specific gene regions. Expanded STRs, depending on the sequence, are located in different parts of the gene. Size of expansion of STRs necessary for the development of individual REDs differ between diseases, however, it may be roughly specified that the longest expansions are located within introns and further within 3′UTRs, middle‐size expansions within 5′UTRs and the shortest within exons, and thus with protein‐coding sequences. Here we show representative REDs from the larger group of diseases. (b) Structures formed by RNA^exp . Trinucleotide CNG repeats form RNA hairpin structures, all characterized by high thermodynamic stability, the highest for CGG, next CAG, and the lowest for CUG repeats. Hairpin structures are also formed by CCUG and G4C2 repeats. Moreover, G4C2 and CGG repeats are able to form G‐quadruplex structure. (c) Protein products derived from repeat‐associated non‐AUG (RAN) translation. RAN translation may potentially start and produce proteins in all three reading frames. In the process of RAN translation of trinucleotide repeats, the homopolymeric proteins with tracts of single amino acids are biosynthesized. CCUG tetranucleotide repeats are RAN translated to proteins containing tracts of four amino acids, the same in all reading frames. RAN translation of G4C2 hexanucleotide repeats is the source of DPRs composed of tracts of two amino acids repeats, one of which is glycine in all reading frames

FIGURE 2

Nuclear processing and accumulation of RNA^exp molecules. (a) Transcription. DSIF and PAF1 complexes promote transcription of repeat expansion regions through inhibition of the formation of DNA secondary structures and R‐loops (described for CAG^exp and G4C2^exp). (b) Splicing. The majority of pre‐mRNAs with expanded repeats undergo correct splicing, however, in some parts of mature transcripts intron retention takes place (described for CCUG^exp and G4C2^exp). Moreover, G4C2^exp‐containing spliced intron is stabilized in a circular form. Bold line, exon; thin line, intron. (c) Sequestration. RNA^exp molecules accumulate in nuclei where they bind multiple RBPs and sequester some of them and form RNA^exp foci (described for CAG^exp, CUG^exp, CCUG^exp, CGG^exp, G4C2^exp). (a–c) Arrow with a dotted line, change in place and/or in time; solid lines show induction or inhibition of certain processes

FIGURE 3

Involvement of RNA^exp in nucleocytoplasmic transport (NCT). (a) Impairment of NCT by RNA^exp . Gradient of RanGDP/RanGTP proteins between nucleus and cytoplasm, supported by RanGAP1, enables proper NCT. Binding of G4C2^exp to RanGAP1 leads to impaired import of nuclear proteins, exemplified by TDP‐43. (b) Export of RNA^exp . Nuclear export adaptor SRSF1 binds to RNA with G4C2^exp and C4G2^exp and supports its transport to cytoplasm through NXF1‐dependent pathway. NXF1 and its cofactor NXT1 participate also in export of circular RNA^exp (circRNA^exp) derived from G4C2^exp‐bearing intron lariat. (a,b) Arrow with a dotted line, change in place and/or in time; solid lines show induction or inhibition of certain processes

FIGURE 4

Processes involving RBPs and RNA^exp in cytoplasm. (a) The role of eIF2D in RAN translation initiation. Non‐canonical translation initiation factor eIF2D delivers Met‐tRNA to the P‐site of 40S ribosomal subunit at CUG codon contributing to RAN translation initiation (described for G4C2^exp). A (aminoacyl) site, P (peptidyl) site, E (exit) site in the ribosome. (b) Elongation of RAN translation. DHX36 helicase unwinds G‐quadruplexes formed by RNA^exp and thus facilitates ribosome processivity and production of toxic homopolymeric proteins or dipeptide repeat proteins (described for G4C2^exp and CGG^exp). (c) RAN translation initiation upon stress. Stress related to the presence of double‐stranded RNA (dsRNA) formed by RNA^exp and RAN proteins activates PKR and PERK kinases, respectively, which catalyze phosphorylation of eIF2α. This, in turn, inhibits eIF2α‐P binding to Met‐tRNA and the formation of preinitiation complex (PIC) with 40S ribosome subunit. Under the stress, eIF2A may take over role of phosphorylated eIF2α‐P, bind Met‐tRNA and participate in translation initiation at near‐cognate start codons (described for G4C2^exp and CCUG^exp). (d) Stress response caused by RNA^exp . RNAi pathway component, ribonuclease Dicer, cleaves dsRNA formed by RNA^exp hairpin or bidirectionally transcribed CUG^exp/CAG^exp duplex into 21‐mer fragments. Such RNA fragments may next activate TLRs and trigger innate immune response. (e) Stress granules formation. Stress stimuli such as RNA^exp and RAN proteins lead to phosphorylation of eIF2α, followed by global translation suppression and formation of stress granules (SG; described for CGG^exp and G4C2^exp). Moreover, G4C2^exp may serve as a core component of SG and promote formation of membraneless organelles composed of different mRNAs and SG protein markers. Chronic stress may entail SG transition towards more solid‐like structures. (f) Phase separation of RNA^exp and RAN protein. Homopolymeric RAN protein, polyG, binds to its own RNA^exp what promotes its phase transition from liquid droplets towards gel‐like aggregates (described for CGG^exp). (a–c) arrow with a dotted line, change in place and/or in time; solid lines show induction or inhibition of certain processes